Beyond average protein secondary structure content prediction using FTIR spectroscopy

This paper demonstrates that secondary structure information beyond purely protein secondary structure content can be predicted from FTIR (Fourier transform infrared spectroscopy) spectra of proteins with a high degree of accuracy. Both neural networks and adaptive neuro-fuzzy inference systems (ANFISs) were employed to predict helix/sheet segment information. The best results were achieved using ANFISs with fuzzy subtractive clustering based on normalised, compressed amide I data with an average SEP (standard error of prediction, root mean of squared errors) of 1.51. Predictions for average helix/sheet length based merely on the amide I band maximum position in combination with the full-width at half-height resulted in a comparable average SEP of 1.62. This suggests the importance of information on the position and width of the amide I band maximum for the prediction of helix/sheet segment information. Finally, the most promising pattern recognition approaches found in this study were applied to a protein with an as yet unknown x-ray structure: native a1-antichymotrypsin (a1-ACT).     

Iron,silicate, and light co-limitation of three Southern Ocean diatom species

The effect of combined iron, silicate, and light co-limitation was investigated in the three diatom species Actinocyclus sp. Ehrenberg, Chaetoceros dichaeta Ehrenberg, and Chaetoceros debilis Cleve, isolated from the Southern Ocean (SO). Growth of all species was co-limited by iron and silicate, reflected in a significant increase in the number of cell divisions compared to the control. Lowest relative Si uptake and drastic frustule malformation was found under iron and silicate co-limitation in C. dichaeta, while Si limitation in general caused cell elongation in both Chaetoceros species. Higher light intensities similar to SO surface conditions showed a negative impact on growth of C. dichaeta and Actinocyclus sp. and no effect on C. debilis. This is in contrast to the assumed light limitation of SO diatoms due to deep wind driven mixing. Our results suggest that growth and species composition of Southern Ocean diatoms is influenced by a sensitive interaction of the abiotic factors, iron, silicate, and light.     

History and evolution of primary productivity studies of the Southern Ocean

The main objective of the article is to give an overview of the history and evolution of phytoplankton research in the Southern Ocean during the past century and a half. It traces the evolution of phytoplankton investigations as it went through several phases commencing with intensive collecting and cataloging and leading to the Discovery investigations with its extensive and detailed studies of Southern Ocean phytoplankton. Following, in the footsteps of the Discovery was the USNS Eltanin with its specialized cruises that centered around the study of the ecology of the primary producers and the dynamics of the lower trophic levels of the food chain. Spurred by the findings of the Eltanin cruises and with the growing concern over the impending exploitation of the Antarctic marine living resources, in particular krill, the BIOMASS program was initiated. The program was the first international collaborative effort to study the dynamic functioning of the Antarctic marine ecosystem. The success of the program has rekindled great international interest in the Southern Ocean which resulted in an explosion of programs such as SO-JGOFS, SO-GLOBEC, EPOS, and several others. In recent years, there has been a major shift in phytoplankton research in the Southern Ocean. This was in response to worldwide concern over the effects of global warming and stratospheric ozone depletion on species diversity, primary production and ecosystem function. This has led to process-oriented programs to study phenomena and processes of global significance in which Antarctica and its surrounding seas play key roles.In an effort to avoid any confusion in the strict usage of terminology, the author has opted to use the Antarctic Ocean and the Southern Ocean interchangeably in this review.     

Kinetics of dissolution of Antarctic diatom frustules and the biogeochemical cycle of silicon in the Southern Ocean

Summary In order to simulate the fate of biogenic silica generated in the surface waters of the Southern Ocean, the dissolution of silica frustules was studied for seven natural assemblages of diatoms, collected during summer 1984 in the Indian sector, and two typical Antarctic diatoms (Nitzschia cylindrus and Chaetoceros deflandrei), following the procedure of Kamatani and Riley (1979). For mean summer conditions in the surface waters of the Southern Ocean (2-3d^-1 for the natural assemblages. The silica frustules trapped by fecal pellets and by gelatinous aggregates, and rapidly transported through the cold waters of the Circumpolar Current, reach the sea bottom of either the continental shelves of the abysses without loosing much of the initial amount of silica (less than 10%). A model based on Stokes' law, modified to take in account of non ideal conditions and of the upwelling rate, is used in order to simulate the fate of silica of unaggregated particles settling down in the cold waters of the Antarctic Divergence. It supports the ideas that 1-the cycle of siliceous particles which radii are <2 m (i.e., of a part of the nanoplankton) is completely achieved in the surface layer, 2-although the biogenic silica of large unaggregated particles (radii over 25 m) may reach the seabottom (within one month to a few years) without complete dissolution, the main explanation for the accumulation of biogenic silica on Antarctic abysses remains transport by fecal pellets and gelatinous aggregates.     

Prediction of moisture, calorific value, ash and carbon content of two dedicated bioenergy crops using near-infrared spectroscopy

The potential of near infrared spectroscopy in conjunction with partial least squares regression to predict Miscanthus xgiganteus and short rotation coppice willow quality indices was examined. Moisture, calorific value, ash and carbon content were predicted with a root mean square error of cross validation of 0.90% (R² = 0.99), 0.13 MJ/kg (R² = 0.99), 0.42% (R² = 0.58), and 0.57% (R² = 0.88), respectively. The moisture and calorific value prediction models had excellent accuracy while the carbon and ash models were fair and poor, respectively. The results indicate that near infrared spectroscopy has the potential to predict quality indices of dedicated energy crops, however the models must be further validated on a wider range of samples prior to implementation. The utilization of such models would assist in the optimal use of the feedstock based on its biomass properties.     

Miocene diatom biostratigraphy at ODP Sites 689, 690, 1088, 1092 (Atlantic sector of the Southern Ocean)

Four ODP sites located between 64°S and 41°S in the eastern Atlantic sector of the Southern Ocean were investigated to refine the Miocene diatom biostratigraphic zonation tied to the geomagnetic chronology. The Miocene diatom stratigraphy from two sites located on Maud Rise (ODP Leg 113) is revised considering the progress in diatom biostratigraphic research, diatom taxonomy and magnetostratigraphic age assignment during the past 10 years. A new diatom zonation was erected for Site 1092 (ODP Leg 177) located on Meteor Rise integrating a magnetostratigraphic interpretation of the shipboard data. This zonation was also applied to Site 1088 (ODP Leg 177) located on Astrid Ridge. The study is focused to Middle and Upper Miocene sequences. It reveals latitudinal differentiations in stratigraphic species ranges and species occurrence pattern that are related to latitudinal differences in surface water masses reflecting the climatic development of the Antarctic cryosphere. Considering the latitudinal differences two stratigraphic zonations are proposed that are applicable to the northern and southern zone of the Southern Ocean, respectively. The southern Southern Ocean Miocene diatom biostratigraphic zonation consists of 16 zones in which 11 represent new or modified zones. The northern biostratigraphic zonation contains 10 diatom zones allowing a stratigraphic resolution in the range of 0.2–2 Myr. This paper also includes the taxonomic transfer of seven Miocene diatom taxa from genus Nitzschia Hassal to Fragilariopsis Hustedt.     

Colonization and community dynamics of class Flavobacteria on diatom detritus in experimental mesocosms based on Southern Ocean seawater

In order to better understand the ecology of microorganisms responsible for secondary production in the Southern Ocean the activity of Flavobacteria communities on diatom detritus in seawater mesocosms was investigated. Seawater was collected from different parts of the Southern Ocean including the Polar Front Zone (PFZ), ice-edge area of the Antarctic Zone (AZ), and a site in the AZ ice pack. Detritus from the cosmopolitan marine diatom Nitzschia closterium Ehrenberg was resuspended in mesocosms containing seawater filtered to remove particulate organic matter, including particle-associated bacteria and most eukaryotes, but retaining native planktonic bacterial assemblages. Mesocosms were incubated at 2 degrees C and samples analysed for changes in community composition using denaturing gradient gel electrophoresis (DGGE), real-time PCR and fluorescent in-situ hybridization (FISH). DGGE banding patterns and FISH images demonstrated rapid bacterial colonization of the detritus, dominated by members of class gamma-Proteobacteria, alpha-Proteobacteria and Flavobacteria. Real-time PCR data indicated members of class Flavobacteria were involved in initial colonization of detrital aggregate, however relative abundance stayed at similar levels found for the original native particle-associated populations. 16S rRNA gene DGGE banding patterns and sequence analysis demonstrated significant variation in Flavobacteria community structure occurred in the first 20 days of the experiment before community stabilization occurred. The community structures between the three mesocosms also markedly differed and major colonizers were primarily derived from detectable members of the initial particle-associated Flavobacteria community, however the abundant uncultured Flavobacteria agg58 clone-related and DE cluster 2 clades, previously identified in Southern Ocean seawater were not observed to colonize the detritus.     

Measuring carbon dynamics in field soils using soil spectral reflectance: prediction of maize root density, soil organic carbon and nitrogen content

This paper reports the development of a proximal sensing technique used to predict maize root density, soil carbon (C) and nitrogen (N) content from the visible and near-infrared (Vis-NIR) spectral reflectance of soil cores. Eighteen soil cores (0?C60?cm depth with a 4.6?cm diameter) were collected from two sites within a field of 90-day-old maize silage; Kairanga silt loam and Kairanga fine sandy loam (Gley Soils). At each site, three replicate soil cores were taken at 0, 15 and 30?cm distance from the row of maize plants (rows were 60?cm apart). Each soil core was sectioned at 5 depths (7.5, 15, 30, 45, and 60?cm) and soil reflectance spectra were acquired from the freshly cut surface at each depth. A 1.5?cm soil slice was taken at each surface to obtain root mass and total soil C and N reference (measured) data. Root densities decreased with depth and distance from plant and were lower in the silt loam, which had the higher total C and N contents. Calibration models, developed using partial least squares regression (PLSR) between the first derivative of soil reflectance and the reference data, were able to predict with moderate accuracy the soil profile root density (r ²?=?0.75; ratio of prediction to deviation [RPD]?=?2.03; root mean square error of cross-validation [RMSECV]?=?1.68?mg/cm³), soil% C (r ²?=?0.86; RPD?=?2.66; RMSECV?=?0.48%) and soil% N (r ²?=?0.81; RPD?=?2.32; RMSECV?=?0.05%) distribution patterns. The important wavelengths chosen by the PLSR model to predict root density were different to those chosen to predict soil C or N. In addition, predicted root densities were not strongly autocorrelated to soil C (r?=?0.60) or N (r?=?0.53) values, indicating that root density can be predicted independently from soil C. This research has identified a potential method for assessing root densities in field soils enabling study of their role in soil organic matter synthesis.     

Climate forcing of diatom productivity in a lowland,eutrophic lake: White Lough revisited

1. In cultural landscapes, lake response to climate can be masked by land‐use change and nutrient loss from their catchments. Palaeolimnological methods were used to reconstruct the ecological response of diatoms in a eutrophic lowland lake (White Lough, Co. Tyrone, Northern Ireland) to altered nutrient P loading and precipitation variability over c. 100 years. 2. ²¹⁰Pb‐dated sediment cores were analysed to determine diatom assemblage variability, biogenic silica concentration, geochemical phosphorus concentration and accumulation rate. Manure P and agricultural N surplus data were collated from documentary sources. Long‐term trends in annual temperature and precipitation were derived from the Armagh Observatory. 3. Diatom community turnover from 1890 until c. 1960 was limited, and assemblages were dominated by Aulacoseira subarctica; after this date, changes primarily reflected a eutrophication sequence owing to increased diffuse nutrient inputs associated with intensification of land use (external P loading increased by a factor of three). 4. Diatom and biogenic Si profiles were compared with North Atlantic Oscillation (NAO) records, an index of regional weather patterns. Biogenic Si exhibited a c. 7‐year cycle, which tracked a cycle of similar timescale in the Armagh climate record for dry summers. In turn, this cycle was related to the variation in the NAO. 5. Monitoring data from 1971 to 2007 of nitrate exports from the Blackwater River showed that these too followed a roughly 7‐year cycle at least up to 2000, in which dry summers were followed by sharp increases in nitrate export. It is argued that diatom production in White Lough reflects the cyclic behaviour in nitrate loading and the constraints that nitrogen availability places on the spring diatom bloom in a lake that is dominated by cyanobacteria.     

FTIR spectroscopy of the complex between pharaonis phoborhodopsin and its transducer protein

pharaonis phoborhodopsin (ppR; also called pharaonis sensory rhodopsin II, psRII) is a photoreceptor for negative phototaxis in Natronobacterium pharaonis. ppR activates the cognate transducer protein, pHtrII, upon absorption of light. ppR and pHtrII form a tight 2:2 complex in the unphotolyzed state, and the interaction is somehow altered during the photocycle of ppR. In this paper, we studied the influence of pHtrII on the structural changes occurring upon retinal photoisomerization in ppR by means of low-temperature FTIR spectroscopy. We trapped the K intermediate at 77 K and compared the ppR(K) minus ppR spectra in the absence and presence of pHtrII. There are no differences in the X-D stretching vibrations (2700-1900 cm(-1)) caused by presence of pHtrII. This result indicates that the hydrogen-bonding network in the Schiff base region is not altered by interaction with pHtrII, which is consistent with the same absorption spectrum of ppR with or without pHtrII. In contrast, the ppR(K) minus ppR infrared difference spectra are clearly influenced by the presence of pHtrII in amide-I (1680-1640 cm(-1)) and amide-A (3350-3250 cm(-1)) vibrations. The identical spectra for the complex of the unlabeled ppR and (13)C- or (15)N-labeled pHtrII indicate that the observed structural changes for the peptide backbone originate from ppR only and are altered by retinal photoisomerization. The changes do not come from pHtrII, implying that the light signal is not transmitted to pHtrII in ppR(K). In addition, we observed D(2)O-insensitive bands at 3479 (-)/3369 (+) cm(-1) only in the presence of pHtrII, which presumably originate from an X-H stretch of an amino acid side chain inside the protein.     

Kinetics of intracellular carbon allocation in a marine diatom

To test models of intracellular carbon flow we measured the labelling kinetics (from ¹⁴CO₂) of major classes of cell polymers (carbohydrate, protein, lipid) and of dissolved organic carbon produced by the marine diatom Thalassiosira pseudonana Hustedt, grown at rates of 0.2 to 2.0·day^?1 under nitrogen or light limitation. Compartmental analysis indicated that tracer carbon quickly entered respiratory and excretory streams, accumulating in the cells at the rate of net production after only 25–50% of cell generation (doubling) time. Respiration rates were low (≤ 0.1 · day^?1) and suggested that illuminated cells in steady-state growth made only minor use of oxidative respiration to support cell synthesis. The tracer was quick to enter all polymers; compartmental analysis indicated that polymer labelling rates were close to the rates of mass synthesis after several hours of incubation with ¹⁴C. Polymer labelling also showed a reallocation of photosynthate from protein to carbohydrate within a few hours of perturbation (shift-down) of nutrient supply in a N-limited chemostat. In steady-state growth, the protein: carbohydrate ratio increased directly with N-limited growth rate but attained its maximum under extreme light-limitation. Carbon flow into the metabolic processes of respiration, excretion and polymer synthesis appeared to be mediated by a small and rapidly cycled pool of substrates under all steady-state growth conditions.     

The impact of phytoplankton on spectral water transparency in the Southern Ocean: implications for primary productivity

Spectral water transparency in the Northern Weddell Sea was studied during Austral spring. The depth of the 1-% surface irradiance level (euphotic depth) varied between 35 and 109 m and was strongly influenced by phytoplankton biomass. Secchi depths were non-linearly related to euphotic depth. In phytoplankton-poor water, the most penetrating spectral region was restricted to a relatively narrow waveband in the blue (488 nm), but the range was broader, between 488 and 525 nm when phytoplankton were abundant. Water transparency in the red spectral range was always low and only to a small extent affected by phytoplankton. Two independent procedures were used to quantify the impact of phytoplankton on spectral water transparency: (1) Regression analysis of spectral in situ vertical light attenuation coefficients in the sea, against coincident chlorophyll concentrations. This method gave chlorophyll-specific light attenuation coefficients; the y-intercept could be interpreted as a measure of light attenuation by pure water plus non-algal material. (2) Spectra of in vivo light absorption derived by spectroscopy, using phytoplankton enriched to varying degrees onto filters. Thus chlorophyll-specific absorption cross-sections were determined. Estimates obtained by both procedures were in close agreement. By integrating over the spectrum of underwater irradiance, in situ chlorophyll-specific absorption cross sections of phytoplankton suspensions, related to all photosynthetically active radiation, were calculated. Light absorption by phytoplankton for photosynthesis is accomplished mainly in the blue spectral range. Also dissolved and particulate organic matter contributed to the attenuation of blue light. Because in water poor in phytoplankton, underwater irradiance was progressively restricted to blue light, chlorophyll-specific absorption cross-sections of phytoplankton, averaged over the spectrum of photosynthetically active irradiance, increased with water depth. In water with elevated phytoplankton biomass, overall light attenuation was generally enhanced. However, because the spectral composition of underwater light changed relatively little with depth, except immediately below the water surface, light absorption cross-sections of phytoplankton changed little below 10 m depth. Vertical differences in the proportions of underwater light absorbed by the phytoplankton community here were mainly dependent on biomass variations. Because of the comparatively small attenuation of blue light by non-algal matter, the efficiency of light harvesting by phytoplankton at any given concentration of chlorophyll in Antractic waters is greater than in other marine regions. At the highest phytoplankton biomass observed by us, as much as 70% of underwater light was available for phytoplankton photosynthesis. When phytoplankton were scarce, <10% of underwater light was harvested by phytoplankton.Contribution within the European Polarstern Study (EPOS), supported by the Deutsche Forschungsgemeinschaft, Grant Ti 115/16-1 to MMT, the European Science Foundation, and by the Alfred Wegener Institut für Polar-und Meeresforschung, Bremerhaven     

Using near-infrared reflectance spectroscopy to predict carbon, nitrogen and phosphorus content in heterogeneous plant material

The aim of this study was to produce calibration equations between near-infrared reflectance (NIR) spectra and the concentrations of carbon, nitrogen, and phosphorus in heterogeneous material: from living needles to litter in Pinus halepensis stands subjected to prescribed burnings. The aim was to determine whether calibrations should be conducted within each stage in the transformation of needles (local calibrations), giving relationships that were accurate but valid only for each particular stage, or whether it was possible to integrate the various forms of variation in needles (global calibrations) while retaining an acceptable accuracy. A principal component analysis calculated from the sample spectral data was used to distinguish three different sets, each sharing spectral characteristics and corresponding to three categories of needle: needles collected on the pines (N), falling needles (F), and litter (L), and each containing samples collected from the burnt sites and a control site. Samples representative of all the forms of variation in spectral properties were selected from within each category and their carbon, nitrogen, and phosphorus concentrations were measured using standard wet chemistry methods; these constituted the calibration sets n, f, and l. Calibrations were produced between the nutrient concentrations and the NIR spectra of the calibration sets n, f, and l and the grouped sets (n+f, f+l, n+f+l). The results of local calibrations made from each individual category showed that the carbon, nitrogen, and phosphorus concentrations were accurately predictable by NIR spectra. The global calibrations made by lumping together several categories were valid for a wider range of concentrations and for spectrally heterogeneous materials and in most cases were just as accurate as the local calibrations produced from each individual category. Received: 2 March 1998 / Accepted: 19 November 1998     

Multivariate FTIR analysis of substrates for protein, polysaccharide, lipid and microbe content: potential for solid-state fermentations

Components of fermentation processes such as protein, polysaccharide and lipid, as well as microbes, such as fungi grown on solid substrates, are difficult to measure in situ. The potential of Fourier Transform Infrared (FTIR) analysis of solid-state fermentations from mid-infrared absorption spectra has been investigated. The problem under consideration was to build a calibration model containing no irrelevant information to enable a multivariate mathematical approach for prediction of component concentrations. Methods for solid sample preparation and preprocessing of FTIR data were developed to assure Beer-Lambert law compliance and produce a well-conditioned multivariate system. The model was tested using composite samples of zein protein, corn starch and azolectin lipid, and corn samples containing known levels of fungal contamination. Preliminary concentration estimates were remarkably close to the correct values, with less than 5% standard error of prediction for all components measured.     

BetaTPred: prediction of beta-TURNS in a protein using statistical algorithms

MOTIVATION: beta-turns play an important role from a structural and functional point of view. beta-turns are the most common type of non-repetitive structures in proteins and comprise on average, 25% of the residues. In the past numerous methods have been developed to predict beta-turns in a protein. Most of these prediction methods are based on statistical approaches. In order to utilize the full potential of these methods, there is a need to develop a web server. RESULTS: This paper describes a web server called BetaTPred, developed for predicting beta-TURNS in a protein from its amino acid sequence. BetaTPred allows the user to predict turns in a protein using existing statistical algorithms. It also allows to predict different types of beta-TURNS e.g. type I, I', II, II', VI, VIII and non-specific. This server assists the users in predicting the consensus beta-TURNS in a protein. AVAILABILITY: The server is accessible from http://imtech.res.in/raghava/betatpred/     

Effects of temperature and water content on the secondary structure of wheat gluten studied by FTIR spectroscopy

The effect of temperature on gluten conditioned at the following water contents, 0%, 13%, and 47% (wet weight basis), was studied by FTIR spectroscopy over the temperature range of 25-85 degrees C. A detailed discussion of the assignment of the amide I band is given. At 0% hydration no changes in the secondary structure with temperature could be detected; spectra were consistent with a tight disordered structure with many protein-protein interactions. At 13% hydration, distinctive changes occurred in the low-frequency region of the amide I band (1,630-1,613 cm(-1)). This was attributed to changes in the beta-sheet structure. On cooling to 25 degrees C, these changes were mainly reversed. It was noted that most of the changes observed occurred above the glass transition temperature. At 47% hydration, more complex changes took place: as the temperature was raised distinct bands at 1,630 and 1,613 cm(-1) merged. However, this process was partially reversed, with recovery of both bands, on cooling. The significance of these results in relation to other changes in gluten proteins in flour and dough with temperature and water content is discussed.     

Detection of insect infestation in museum objects by carbon dioxide measurement using FTIR

Detecting the presence of active insects in various stages of their lifecycle within an art object is often difficult in the absence of direct visualization of the insect. It usually relies on one's ability to assess the evidence of their activity around, on, or in the object. To augment this “eyeball” method, a Fourier transform infrared spectroscopy system was used to determine the presence of the insect through its respired gas, carbon dioxide. The application of the procedure to assist in control of insect infestation within art objects is described. Two instruments are discussed in this paper. The prototype instrument could detect a change in carbon dioxide that was 0.3–0.4 ppm/h and required days to reliably determine this level. The second instrument could detect changes as low as 0.09 ppm/h and could provide results in only 4 h. Carbon dioxide measurements were collected from representative insect groups that have caused problems in art objects; these were worker termites (Reticulitermes sp.), carpet beetle adult and larvae (Anthrenus sp.), an odd beetle larva (Thylodrias sp.) and a mature silverfish (Lepisma sp.), as well as selected museum art objects composed of wood, fabric, and/or feathers suspected of harboring insects.     

SVM-based method for protein structural class prediction using secondary structural content and structural information of amino acids

The knowledge collated from the known protein structures has revealed that the proteins are usually folded into the four structural classes: all-α, all-β, α/β and α + β. A number of methods have been proposed to predict the protein's structural class from its primary structure; however, it has been observed that these methods fail or perform poorly in the cases of distantly related sequences. In this paper, we propose a new method for protein structural class prediction using low homology (twilight-zone) protein sequences dataset. Since protein structural class prediction is a typical classification problem, we have developed a Support Vector Machine (SVM)-based method for protein structural class prediction that uses features derived from the predicted secondary structure and predicted burial information of amino acid residues. The examination of different individual as well as feature combinations revealed that the combination of secondary structural content, secondary structural and solvent accessibility state frequencies of amino acids gave rise to the best leave-one-out cross-validation accuracy of ~81% which is comparable to the best accuracy reported in the literature so far.     

The role of the chaetognath Sagitta gazellae in the vertical carbon flux of the Southern Ocean

Chaetognaths are among the most abundant predators in the Southern Ocean and are potentially important components in the biological carbon pump due to the production of large, fast-sinking fecal pellets. In situ S. gazellae abundance, fecal pellet production, sinking rates, carbon content, and vertical carbon fluxes were measured at the Lazarev Sea between December 2005 and January 2006. Sagitta gazellae produce fecal pellets that sink at speeds of 33–600 m day⁻¹ and have carbon contents of 0.01–0.8 mg C pellet⁻¹. Vertical carbon flux was later compared with the total carbon flux measured at 360 m depth at the study area. Rough estimates using published seasonal abundance of S. gazellae indicate that, at 360 m depth in the Lazarev Sea, this specie may contribute 12 and 5% of the total vertical carbon flux in winter (ice-covered) and summer (ice-free), respectively. Thus, the role of chaetognaths in the downward transport of organic matter may be far more important than previously thought.